Density of fecal coliforms (FC) such as Escherichia coli is the most commonly used indicator of fecal pathogen content of biosolids. When biosolids are disposed off or used for soil amendment, they pose public health risks. So far anaerobic digesters have been considered to be an effective treatment option for pathogen and FC reduction in biosolids. However, recent studies revealed that there is a significant re-growth and reactivation of indicator organisms in biosolids upon dewatering by centrifugation. Although the exact mechanism of FC reactivation is yet to be understood, a few extensive recent studies strongly suggest that FC go into a viable but non-culturable (VBNC) state during anaerobic digestion. Therefore, quantitative detection of live cells among the total in biosolids samples, without using culturing-based approaches, is highly critical from a public health risk assessment perspective. Since recent investigations proved the significant re-growth and reactivation of indicator organisms. Persistence of DNA in the environment after cell death in the range of days to weeks limits the application of DNA-based approaches for the detection of live bacteria. Using selective nucleic acid intercalating dyes such as ethidium monoazide (EMA) and propidium monoazide (PMA) is one of the alternative approaches to detect and quantify the viable cells by quantitative PCR. These compounds have the ability to penetrate only into dead cells with compromised membrane integrity. They intercalate in the DNA via photo-inducible azide groups and in turn inhibit DNA amplification during PCR reactions. PMA has been successfully used in different studies and microorganisms but it has not been evaluated sufficiently for the complex environmental samples such as biosolids. In this study Escherichia coli ATCC 25922 and uidA gene were used as model organism and as target sequence respectively in absolute quantification method with real-time PCR. Experiments with the known quantities of live and dead cell mixtures showed that PMA treatment inhibits PCR amplification from dead cells with over 99% efficiency. The results of this study conclusively demonstrated that PMA-modified PCR could be successfully applied to the biosolids when total suspended solid (TSS) concentration is 2000 mg/L or below.

Development of the advanced, real-time methods for monitoring of bioaerosols is becoming increasingly important. At present, the Ultraviolet Aerodynamic Particle Sizer (UVAPS, Model 3312, TSI, St. Paul., MN) is the only commercially available method for in-situ, continuous measurements of viable airborne microorganisms. Research included in this thesis aimed towards comprehensive evaluation of the method over a wide range of operating conditions, linking the experimental results to the theoretical basis of its design and operation, and to developing a scientific basis for its application to real-time monitoring of bioaerosols. Specifically, due to a growing concern in the general community about the environmental and health aspects of biological aerosols originated from various types of agricultural operations including animal farming, this research was focussed on developing a research methodology/strategy for applying the method to the investigation of bioaerosols in the swine confinement buildings (SCB). Investigations under controlled laboratory conditions were primarily concerned with selectivity, sensitivity, counting efficiency, and detection limits of the spectrometer. This study also examined the effect of physiological state (metabolic activity) of bacteria on the performance characteristics of the method. The practical implications of the research findings are discussed in this thesis. Further field investigations undertaken on a pig farm advanced understanding of the UVAPS performance in the real-life environmental settings. The research also provided a new insight on the particle size distribution and the effect of on-farm-activities on aerosol load inside the SCBs, for both biological and non-biological aerosols. This study has proved that the UVAPS is a powerful tool for investigation of viable bioaerosols in the environment. However, this method is limited to detection of active metabolising bacteria that excludes dormant bacterial spores. In addition, the method is very sensitive to physiological state of bacteria and to the effect of adverse environmental conditions on metabolic activity of airborne bacteria, which may decrease the amount of the intrinsic fluorophores in the cells below sensitivity level iv of the monitor. Possible limitations of this technology include also the lack of selectivity and thus interferences from the non-microbial organic components of airborne particles. In addition, the sensitivity of the method is insufficient for monitoring viable bacteria in the environments with relatively low concentrations of bioaerosols. In order to increase sensitivity of the method, it would be desirable to concentrate the bioaerosols into a smaller volume with the aim of high-volume virtual impactors (aerosol concentrators) prior to the monitoring. Therefore, in the indoor environments where an application of the concentrator is not feasible, the utilisation of the UVAPS may be problematic. Due to the intrinsic limitations, the method is not recommended for the direct measurements of viable bioaerosols and should be used in conjunction with the conventional biosamplers for obtaining more realistic insights into the microbial air quality. Nevertheless, the UVAPS has been found to be an adequate method for the investigation of the dynamics of biological aerosols in real-time. Overall, this thesis contributes to the advancing of the understanding of the method and may assist in developing new, more advanced technologies for the real-time monitoring of viable bioaerosols, as well as in developing sampling strategies for the application of the method to various bioaerosol studies.

The Intelligent Control Paradigm for software architecture is the result of this work. The Viable Software Approach is developed as an instance of the paradigm. The approach uses the Viable System Model as the basis for software system architecture. The result is a model-based architecture and approach for developing software systems by piecemeal adaptation with the goal that they become adaptive systems at runtime. Software built in this manner is called Viable Software. Viable Software represents a unifying class of self-controlling software that is an “intelligent” control system. Cybernetics, Control Theory, and Complexity Theory are the background for this work, and aspects relevant to this work are presented. These results are related to software architecture and software engineering. Rationale for the selection of the Viable System Model as a basis for software systems is given. The Viable System Model is described. The model is restated as an Alexanderian “pattern language” to make it more accessible to software engineering. A Viable Software Approach is proposed and expressed in the form of a Product Line Architecture that arranges the Viable System Model, the Viable Software Architecture, a Viable Component Framework, and a Component Transfer Protocol into a system for generative programming. An important result is the formalisation of the pattern of the Viable System into the interface specifications of the Viable Component. Three case studies illustrate the approach. The first is an analysis and extension of the Groove collaboration system. This study shows how the approach is used to map an existing system into the Viable Software Architecture and add fuzzy-adaptive user interface controllers. The second study presents the design and detailed software construction of an adaptive camera controller as part of a smart environment. The final study shows how a Business-to-Business e-Commerce system can be evolved and an expert system-based controller developed to implement business contracts.

The Intelligent Control Paradigm for software architecture is the result of this work. The Viable Software Approach is developed as an instance of the paradigm. The approach uses the Viable System Model as the basis for software system architecture. The result is a model-based architecture and approach for developing software systems by piecemeal adaptation with the goal that they become adaptive systems at runtime. Software built in this manner is called Viable Software. Viable Software represents a unifying class of self-controlling software that is an “intelligent” control system. Cybernetics, Control Theory, and Complexity Theory are the background for this work, and aspects relevant to this work are presented. These results are related to software architecture and software engineering. Rationale for the selection of the Viable System Model as a basis for software systems is given. The Viable System Model is described. The model is restated as an Alexanderian “pattern language” to make it more accessible to software engineering. A Viable Software Approach is proposed and expressed in the form of a Product Line Architecture that arranges the Viable System Model, the Viable Software Architecture, a Viable Component Framework, and a Component Transfer Protocol into a system for generative programming. An important result is the formalisation of the pattern of the Viable System into the interface specifications of the Viable Component. Three case studies illustrate the approach. The first is an analysis and extension of the Groove collaboration system. This study shows how the approach is used to map an existing system into the Viable Software Architecture and add fuzzy-adaptive user interface controllers. The second study presents the design and detailed software construction of an adaptive camera controller as part of a smart environment. The final study shows how a Business-to-Business e-Commerce system can be evolved and an expert system-based controller developed to implement business contracts.

The Intelligent Control Paradigm for software architecture is the result of this work. The Viable Software Approach is developed as an instance of the paradigm. The approach uses the Viable System Model as the basis for software system architecture. The result is a model-based architecture and approach for developing software systems by piecemeal adaptation with the goal that they become adaptive systems at runtime. Software built in this manner is called Viable Software. Viable Software represents a unifying class of self-controlling software that is an “intelligent” control system. Cybernetics, Control Theory, and Complexity Theory are the background for this work, and aspects relevant to this work are presented. These results are related to software architecture and software engineering. Rationale for the selection of the Viable System Model as a basis for software systems is given. The Viable System Model is described. The model is restated as an Alexanderian “pattern language” to make it more accessible to software engineering. A Viable Software Approach is proposed and expressed in the form of a Product Line Architecture that arranges the Viable System Model, the Viable Software Architecture, a Viable Component Framework, and a Component Transfer Protocol into a system for generative programming. An important result is the formalisation of the pattern of the Viable System into the interface specifications of the Viable Component. Three case studies illustrate the approach. The first is an analysis and extension of the Groove collaboration system. This study shows how the approach is used to map an existing system into the Viable Software Architecture and add fuzzy-adaptive user interface controllers. The second study presents the design and detailed software construction of an adaptive camera controller as part of a smart environment. The final study shows how a Business-to-Business e-Commerce system can be evolved and an expert system-based controller developed to implement business contracts.

The Intelligent Control Paradigm for software architecture is the result of this work. The Viable Software Approach is developed as an instance of the paradigm. The approach uses the Viable System Model as the basis for software system architecture. The result is a model-based architecture and approach for developing software systems by piecemeal adaptation with the goal that they become adaptive systems at runtime. Software built in this manner is called Viable Software. Viable Software represents a unifying class of self-controlling software that is an “intelligent” control system. Cybernetics, Control Theory, and Complexity Theory are the background for this work, and aspects relevant to this work are presented. These results are related to software architecture and software engineering. Rationale for the selection of the Viable System Model as a basis for software systems is given. The Viable System Model is described. The model is restated as an Alexanderian “pattern language” to make it more accessible to software engineering. A Viable Software Approach is proposed and expressed in the form of a Product Line Architecture that arranges the Viable System Model, the Viable Software Architecture, a Viable Component Framework, and a Component Transfer Protocol into a system for generative programming. An important result is the formalisation of the pattern of the Viable System into the interface specifications of the Viable Component. Three case studies illustrate the approach. The first is an analysis and extension of the Groove collaboration system. This study shows how the approach is used to map an existing system into the Viable Software Architecture and add fuzzy-adaptive user interface controllers. The second study presents the design and detailed software construction of an adaptive camera controller as part of a smart environment. The final study shows how a Business-to-Business e-Commerce system can be evolved and an expert system-based controller developed to implement business contracts.

The Intelligent Control Paradigm for software architecture is the result of this work. The Viable Software Approach is developed as an instance of the paradigm. The approach uses the Viable System Model as the basis for software system architecture. The result is a model-based architecture and approach for developing software systems by piecemeal adaptation with the goal that they become adaptive systems at runtime. Software built in this manner is called Viable Software. Viable Software represents a unifying class of self-controlling software that is an “intelligent” control system. Cybernetics, Control Theory, and Complexity Theory are the background for this work, and aspects relevant to this work are presented. These results are related to software architecture and software engineering. Rationale for the selection of the Viable System Model as a basis for software systems is given. The Viable System Model is described. The model is restated as an Alexanderian “pattern language” to make it more accessible to software engineering. A Viable Software Approach is proposed and expressed in the form of a Product Line Architecture that arranges the Viable System Model, the Viable Software Architecture, a Viable Component Framework, and a Component Transfer Protocol into a system for generative programming. An important result is the formalisation of the pattern of the Viable System into the interface specifications of the Viable Component. Three case studies illustrate the approach. The first is an analysis and extension of the Groove collaboration system. This study shows how the approach is used to map an existing system into the Viable Software Architecture and add fuzzy-adaptive user interface controllers. The second study presents the design and detailed software construction of an adaptive camera controller as part of a smart environment. The final study shows how a Business-to-Business e-Commerce system can be evolved and an expert system-based controller developed to implement business contracts.

The Intelligent Control Paradigm for software architecture is the result of this work. The Viable Software Approach is developed as an instance of the paradigm. The approach uses the Viable System Model as the basis for software system architecture. The result is a model-based architecture and approach for developing software systems by piecemeal adaptation with the goal that they become adaptive systems at runtime. Software built in this manner is called Viable Software. Viable Software represents a unifying class of self-controlling software that is an “intelligent” control system. Cybernetics, Control Theory, and Complexity Theory are the background for this work, and aspects relevant to this work are presented. These results are related to software architecture and software engineering. Rationale for the selection of the Viable System Model as a basis for software systems is given. The Viable System Model is described. The model is restated as an Alexanderian “pattern language” to make it more accessible to software engineering. A Viable Software Approach is proposed and expressed in the form of a Product Line Architecture that arranges the Viable System Model, the Viable Software Architecture, a Viable Component Framework, and a Component Transfer Protocol into a system for generative programming. An important result is the formalisation of the pattern of the Viable System into the interface specifications of the Viable Component. Three case studies illustrate the approach. The first is an analysis and extension of the Groove collaboration system. This study shows how the approach is used to map an existing system into the Viable Software Architecture and add fuzzy-adaptive user interface controllers. The second study presents the design and detailed software construction of an adaptive camera controller as part of a smart environment. The final study shows how a Business-to-Business e-Commerce system can be evolved and an expert system-based controller developed to implement business contracts.

Bacteriophages are viruses that specifically infect bacteria. The bactericidal nature of lytic bacteriophages has been exploited by scientists for decades with the hope to utilise them in the fight against bacterial infections and antibiotic resistant bacteria in medical settings. More recently, the potential applications of bacteriophages for biocontrol in the agrifood and environmental sectors have been investigated in an attempt to develop ‘natural’ antimicrobial products. Bacteriophages have a couple of decisive advantages over conventional methods of controlling pathogenic bacteria, such as high host specificity, the ability to self-replicate, and the ability to evolve with their hosts. However, more research is needed to optimise the parameters for phage applications, including the impact of environmental conditions on lysis efficiency, multiplicity of infection, and to significantly minimise the emergence of bacterial resistance to phages. Temperature plays a key role in every biological activity in nature. It is also assumed that temperature has an effect on phage lysis efficiency. A comprehensive study of it and how it affects both the host cells and their corresponding phages is crucial to ensure the efficient removal of bacterial pathogens. In this thesis, temperature (as selected parameter) was investigated to determine its influence on the lysis effectiveness of the three different phages belonging to the family of the Myoviridea that were isolated and purified from a single water sample taken from a brook receiving treated wastewater. We used the multiplicity of infection of 1 in all of our study in this project. Temperature was found to have a significant impact on phage-mediated lysis efficiency. Both the temperature of incubation of the phage-bacteria mixture (incubation temperature) and the temperature history of bacterial hosts were found to have profound effects on plaque sizes as well as plaque numbers. Plaque size and number decreased with increasing temperature. For the phages examined, bacterial lysis was more efficient at 20°C compared to 30 or 37°C. Phages were suggested to be well adapted to the environment where they were isolated from with general implications for use in biological disinfection. Furthermore, the temperature history of the bacteria (prior to phage encounter) was found to have a modulating effect on their susceptibility to lysis. A second part of this study compared the performance of the three phages in regard to bacterial resistance. The emergence of bacterial resistance is a major obstacle to the success of bacteriophages applications. The use of multiple phages is typically recommended and has proven better than the use of a single phage. However, the bestway to perform phage treatment is still very unclear. This study therefore compared simultaneous addition of multiple phages (in form of a cocktail) with the sequential addition of the individual phages at different time points in trying to delay the emergence of bacterial resistance. The data obtained from this work suggest that lysis effectiveness can be adjusted to optimize any treatment goal. For fast initial bacterial clearance the use of a single phage with short time maximal lysis efficiency proved most efficient, while the simultaneous addition of phages in the form of a cocktail was most successful strategy in our study. Addition of selected phages sequentially can be normalized in such a way that is just as effective as a cocktail. A third part of this thesis looked into the susceptibility of bacteria that had undergone sublethal disinfection. We addressed the question whether bacteria subjected to sublethal doses of chlorine and UV are still susceptible to phage-mediated lysis. The chlorine treatments indicated the development of a phage-insensitive phenotype for a critical chlorine dose in the transition zone between live and dead. The remaining live (and culturable) bacteria were shown insensitive to the selected phage. The lowest UV exposure at 2.8 mJ/cm2 eliminated bacteria susceptibility to the phages. This phage- resistant phenotype may have serious consequences for the application of phages on foods or water that have previously undergone a weak disinfection regime.

abstract: ABSTRACT This mixed methods study examined how a high-poverty urban school district implemented four initiatives to support special education teachers and increase student achievement. The initiatives that were implemented consisted of direct instruction teaching methods, the use of a district-approved curriculum, monitoring program fidelity with walkthroughs, and increased professional development opportunities. Quantitatively, the study compared walkthrough data and student achievement scores. The walkthrough data was collected from 52 special education teachers employed at the 19 schools making up the district while teaching reading and math. Student achievement scores were collected from the students taught by the 52 special education teachers. The walkthrough data compared the percentage of students making academic growth on district assessments with the percentage of teachers implementing the district initiatives with a high level of fidelity. Data was collected and analyzed between the first and third quarters of the 2013–2014 school year. Qualitatively, six special education teachers were interviewed to examine their thoughts on the change process and to determine their needs to be successful as they continued to implement the district initiatives. The results of the quantitative data indicated that students demonstrated growth as walkthrough scores increased in 16 out of 19 schools, specifically in the area of math. Fidelity to the initiatives increased throughout the year as teachers began to use and implement the initiatives. The results of the qualitative data indicated that special education teachers positively responded to the support they received through the Special Services ii Department and the district’s initiatives. Using grounded theory, it was determined that teachers need opportunities for collaboration, feedback, and time to practice in order to be successful. Lastly, the epilogue discusses the next steps that are being taken by the district to support all students with their learning needs. / Dissertation/Thesis / Appendix G--Contains Qualitative and Quantitative Data Used in the Study / Doctoral Dissertation Educational Administration and Supervision 2015